9S4Z | pdb_00009s4z

AcuB from Geobacillus stearothermophilus with AMP and ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10% PEG 20000, 100 mM MES pH 6.5, soaked 30 min in 5 mM AMP + 5 mM ADP cryo: 10% PEG 20000, 15% PEG 400, 100 mM MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.59	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.298	α = 90
b = 96.668	β = 90
c = 101.381	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	double mirror	2025-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.05960	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.62	50	97.5	0.071	0.074	0.999	21	12.7		15706		-3	72.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.62	2.78	84.6		0.702	0.745	0.838	2.22	8.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.62	48.381	15660	808	97.655	0.184	0.1814	0.1785	0.2353	0.2336	78.689

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
4.934			-0.564		-4.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.13
r_dihedral_angle_6_deg	14.315
r_lrange_it	11.352
r_lrange_other	11.325
r_scangle_it	9.61
r_scangle_other	9.608
r_dihedral_angle_2_deg	8.622
r_mcangle_it	7.644
r_mcangle_other	7.644
r_scbond_it	6.712
r_scbond_other	6.71
r_dihedral_angle_1_deg	6.451
r_mcbond_it	5.575
r_mcbond_other	5.575
r_angle_refined_deg	1.701
r_angle_other_deg	0.544
r_symmetry_nbd_refined	0.285
r_nbd_other	0.26
r_nbd_refined	0.24
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.131
r_ncsr_local_group_1	0.106
r_dihedral_angle_other_2_deg	0.097
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3099
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing